Remove unused arguments, replace mutable defaults

Closes https://github.com/jensengroup/propka/issues/53
Closes https://github.com/jensengroup/propka/issues/56

propka/iterative.py

@@ -202,7 +202,7 @@ def add_iterative_ion_pair(object1: "Iterative", object2: "Iterative",
                 object2.determinants['sidechain'].append(interaction)
 
 
-def add_determinants(iterative_interactions: List[Interaction], version: Version, _=None):
+def add_determinants(iterative_interactions: List[Interaction], version: Version):
     """Add determinants iteratively.
 
     The iterative pKa scheme. Later it is all added in 'calculateTotalPKA'

propka/lib.py

@@ -8,10 +8,11 @@ Implements many of the main functions used to call PROPKA.
 import logging
 import argparse
 from pathlib import Path
-from typing import Iterable, Iterator, List, TYPE_CHECKING, NoReturn, Optional, Tuple, TypeVar
+from typing import Dict, Iterable, Iterator, List, TYPE_CHECKING, NoReturn, Optional, Tuple, TypeVar
 
 if TYPE_CHECKING:
     from propka.atom import Atom
+    from propka.conformation_container import ConformationContainer
 
 
 T = TypeVar("T")
@@ -46,7 +47,8 @@ class Options:
     window: Tuple[float, float, float] = (0.0, 14.0, 1.0)
 
 
-def protein_precheck(conformations, names):
+def protein_precheck(conformations: Dict[str, "ConformationContainer"],
+                     names: Iterable[str]):
     """Check protein for correct number of atoms, etc.
 
     Args:
@@ -55,7 +57,7 @@ def protein_precheck(conformations, names):
     for name in names:
         atoms = conformations[name].atoms
         # Group the atoms by their residue:
-        atoms_by_residue = {}
+        atoms_by_residue: Dict[str, List[Atom]] = {}
         for atom in atoms:
             if atom.element != 'H':
                 res_id = resid_from_atom(atom)

propka/molecular_container.py

@@ -195,7 +195,7 @@ class MolecularContainer:
             stability_range = (min(stable_values), max(stable_values))
         return profile, opt, range_80pct, stability_range
 
-    def get_charge_profile(self, conformation: str = 'AVR', grid=[0., 14., .1]):
+    def get_charge_profile(self, conformation: str = 'AVR', grid=(0., 14., .1)):
         """Get charge profile for conformation as function of pH.
 
         Args:
@@ -212,13 +212,13 @@ class MolecularContainer:
             charge_profile.append([ph, q_unfolded, q_folded])
         return charge_profile
 
-    def get_pi(self, conformation: str = 'AVR', grid=[0., 14., 1], *,
+    def get_pi(self, conformation: str = 'AVR', grid=(0., 14.), *,
                precision: float = 1e-4) -> Tuple[float, float]:
         """Get the isoelectric points for folded and unfolded states.
 
         Args:
             conformation:  conformation to test
-            grid:  grid of pH values [min, max, step]
+            grid:  pH window [min, max]
             precision:  Compute pI up to this precision
         Returns:
             1. Folded state PI

propka/output.py

@@ -14,7 +14,7 @@ from datetime import date
 from decimal import Decimal
 from os import PathLike
 from pathlib import Path
-from typing import IO, AnyStr, List, Optional, Union, TYPE_CHECKING
+from typing import IO, AnyStr, List, Optional, Tuple, Union, TYPE_CHECKING
 import warnings
 
 from .parameters import Parameters
@@ -75,22 +75,19 @@ def write_pdb_for_conformation(conformation: "ConformationContainer",
 def write_pka(protein: "MolecularContainer",
               parameters: Parameters,
               filename: Optional[_PathArg] = None,
-              conformation='1A',
+              conformation: str = '1A',
-              reference="neutral", _="folding", verbose=False,
+              reference: str = "neutral",
-              __=None):
+              *,
+              verbose: bool = True):
     """Write the pKa-file based on the given protein.
 
     Args:
         protein:  protein object
         filename:  output file name
-        conformation:  TODO - figure this out
+        conformation: specific conformation
         reference:  reference state
-        _:  "folding" or other
         verbose:  Boolean flag for verbosity
-        __:  options object
     """
-    # TODO - the code immediately overrides the verbose argument; why?
-    verbose = True
     if filename is None:
         filename = "{0:s}.pka".format(protein.name)
     if verbose:
@@ -196,8 +193,11 @@ def get_summary_section(protein: "MolecularContainer", conformation: str,
 
 def get_folding_profile_section(
         protein: "MolecularContainer",
-        conformation='AVR', direction="folding", reference="neutral",
+        conformation: str = 'AVR',
-        window=[0., 14., 1.0], _=False, __=None):
+        direction: str = "folding",
+        reference: str = "neutral",
+        window: Tuple[float, float, float] = (0., 14., 1.),
+):
     """Returns string with the folding profile section of the results.
 
     Args:
@@ -206,8 +206,6 @@ def get_folding_profile_section(
         direction:  'folding' or other
         reference:  reference state
         window:  pH window [min, max, step]
-        _:  Boolean for verbose output
-        __:  options object
     Returns:
         string
     """
@@ -253,7 +251,8 @@ def get_folding_profile_section(
     return str_
 
 
-def get_charge_profile_section(protein, conformation='AVR', _=None):
+def get_charge_profile_section(protein: "MolecularContainer",
+                               conformation: str = 'AVR'):
     """Returns string with the charge profile section of the results.
 
     Args: